PDBsum entry 5ens

Transport protein

PDB id: 5ens

Contents

Protein chains

580 a.a.

156 a.a.

Ligands

RHQ

Waters ×253

PDB id:

5ens

Name:

Transport protein

Title:

Rhodamine bound structure of bacterial efflux pump.

Structure:

Multidrug efflux pump subunit acrb,multidrug efflux pump subunit acrb. Chain: a, b, c. Synonym: acrab-tolc multidrug efflux pump subunit acrb,acridine resistance protein b,acrab-tolc multidrug efflux pump subunit acrb, acridine resistance protein b. Engineered: yes. Darpin. Chain: d, e, f.

Source:

Escherichia coli k-12. Organism_taxid: 83333. Gene: acrb, acre, b0462, jw0451. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.80Å R-factor: 0.197 R-free: 0.258

Authors:

H.Sjuts,A.R.Ornik,K.M.Pos

Key ref:

H.Sjuts et al. (2016). Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives. Proc Natl Acad Sci U S A, 113, 3509-3514. PubMed id: 26976576 DOI: 10.1073/pnas.1602472113

Date:

09-Nov-15 Release date: 06-Apr-16

Protein chains

P31224  (ACRB_ECOLI) -  Multidrug efflux pump subunit AcrB from Escherichia coli (strain K12)

Seq: 1049 a.a.

Struc: 580 a.a.

Protein chains

No UniProt id for this chain

Struc: 156 a.a.

DOI no: 10.1073/pnas.1602472113

Proc Natl Acad Sci U S A 113:3509-3514 (2016)

PubMed id: 26976576

Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives.

H.Sjuts, A.V.Vargiu, S.M.Kwasny, S.T.Nguyen, H.S.Kim, X.Ding, A.R.Ornik, P.Ruggerone, T.L.Bowlin, H.Nikaido, K.M.Pos, T.J.Opperman.

ABSTRACT

TheEscherichia coliAcrAB-TolC efflux pump is the archetype of the resistance nodulation cell division (RND) exporters from Gram-negative bacteria. Overexpression of RND-type efflux pumps is a major factor in multidrug resistance (MDR), which makes these pumps important antibacterial drug discovery targets. We have recently developed novel pyranopyridine-based inhibitors of AcrB, which are orders of magnitude more powerful than the previously known inhibitors. However, further development of such inhibitors has been hindered by the lack of structural information for rational drug design. Although only the soluble, periplasmic part of AcrB binds and exports the ligands, the presence of the membrane-embedded domain in AcrB and its polyspecific binding behavior have made cocrystallization with drugs challenging. To overcome this obstacle, we have engineered and produced a soluble version of AcrB [AcrB periplasmic domain (AcrBper)], which is highly congruent in structure with the periplasmic part of the full-length protein, and is capable of binding substrates and potent inhibitors. Here, we describe the molecular basis for pyranopyridine-based inhibition of AcrB using a combination of cellular, X-ray crystallographic, and molecular dynamics (MD) simulations studies. The pyranopyridines bind within a phenylalanine-rich cage that branches from the deep binding pocket of AcrB, where they form extensive hydrophobic interactions. Moreover, the increasing potency of improved inhibitors correlates with the formation of a delicate protein- and water-mediated hydrogen bond network. These detailed insights provide a molecular platform for the development of novel combinational therapies using efflux pump inhibitors for combating multidrug resistant Gram-negative pathogens.